CI: Apply Copier template

.auto-changelog

@@ -3,7 +3,7 @@
     "template": ".auto-changelog-template.hbs",
     "commitLimit": false,
     "backfillLimit": false,
-    "ignoreCommitPattern": "Release [0-9]+\\.[0-9]+\\.[0-9]+|Update CHANGELOG.*|.*\\[skip-changelog\\].*|\\[pre-commit.ci\\]",
+    "ignoreCommitPattern": "Release:? [0-9]+\\.[0-9]+\\.[0-9]+|Update CHANGELOG.*|.*\\[skip-changelog\\].*|\\[pre-commit.ci\\]",
     "commitUrl": "https://github.com/BlueBrain/NeuroTS/commit/{id}",
     "issueUrl": "https://github.com/BlueBrain/NeuroTS/issues/{id}",
     "mergeUrl": "https://github.com/BlueBrain/NeuroTS/pull/{id}",

.auto-changelog-template.hbs

@@ -9,6 +9,7 @@ Introduction
 • The types feat:, fix:, chore:, docs:, refactor:, test:, style:, perf: must be at the beginning of the commit subject with an : on end.
    • They can optionally have a scope set to outline the module or component that is affected eg feat(bldAssess):
 • There is a short hash on the end of every commit that is currently commented out so that change log did not grow too long (due to some system's file size limitations).  You can uncomment if you wish [`{{shorthash}}`]({{href}})
+
 Example Definitions
 • feat: A new feature
 • fix: A bug fix
@@ -30,6 +31,8 @@ Example Definitions
     "replaceText": {
       "([bB]reaking:)": "",
       "([bB]reaking change:)": "",
+      "(^[bB]uild:)": "",
+      "(^[bB]uild\\()": "\\(",
       "(^[fF]eat:)": "",
       "(^[fF]eat\\()": "\\(",
       "(^[fF]ix:)": "",
@@ -59,7 +62,7 @@ Example Definitions
  \s = whitespace
  . = any character except newline
  | = or
- [aA] = charcter a or character A
+ [aA] = character a or character A
  --}}
 
 
@@ -87,7 +90,11 @@ Example Definitions
   {{/commit-list}}
 
   {{! List commits organised under a heading, but not those already listed in the breaking section }}
-      {{#commit-list merges heading='### New Features' message='^[fF]eat:|[fF]eat\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
+      {{#commit-list merges heading='### Build' message='^[bB]uild:|^[bB]uild\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
+        - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
+      {{/commit-list}}
+
+      {{#commit-list merges heading='### New Features' message='^[fF]eat:|^[fF]eat\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
@@ -123,7 +130,7 @@ Example Definitions
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
-      {{#commit-list merges heading='### Uncategorized Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
+      {{#commit-list merges heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild\(|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
         - {{message}} ({{author}}{{#if href}} - [#{{id}}]({{href}}){{/if}})
       {{/commit-list}}
 
@@ -133,7 +140,11 @@ Example Definitions
   {{/commit-list}}
 
   {{! List commits organised under a heading, but not those already listed in the breaking section }}
-      {{#commit-list commits heading='### New Features' message='^[fF]eat:|[fF]eat\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
+      {{#commit-list commits heading='### Build' message='^[bB]uild:|^[bB]uild\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
+        - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
+      {{/commit-list}}
+
+      {{#commit-list commits heading='### New Features' message='^[fF]eat:|^[fF]eat\(' exclude='[bB]reaking [cC]hange:|[bB]reaking:|\[skip-changelog\]'}}
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 
@@ -169,7 +180,7 @@ Example Definitions
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 
-      {{#commit-list commits heading='### Uncategorized Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
+      {{#commit-list commits heading='### General Changes' exclude='[bB]reaking [cC]hange:|[bB]reaking:|^[bB]uild:|^[bB]uild\(|^[fF]eat:|^[fF]eat\(|^[fF]ix:|^[fF]ix\(|^[cC]hore:|^[cC]hore\(|^[cC][iI]:|^[cC][iI]\(|^[dD]ocs:|^[dD]ocs\(|^[rR]efactor:|^[rR]efactor\(|^[tT]est:|^[tT]est\(|^[sS]tyle:|^[sS]tyle\(|^[pP]erf:|^[pP]erf\(|\[skip-changelog\]'}}
         - {{subject}} ({{author}}{{#if href}} - [{{shorthash}}]({{href}}){{/if}})
       {{/commit-list}}
 

.copier-answers.yml

@@ -1,6 +1,6 @@
 # Changes here will be overwritten by Copier
 
-_commit: 0.1.9
+_commit: 0.1.33
 _src_path: git@bbpgitlab.epfl.ch:neuromath/python-template.git
 author_email: ''
 author_name: Blue Brain Project, EPFL

.gitattributes

@@ -1 +1,3 @@
 *.asc linguist-detectable=false
+.auto-changelog-template.hbs linguist-detectable=false
+commitlint.config.js linguist-detectable=false

.github/dependabot.yml

@@ -0,0 +1,13 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  # Configure check for outdated GitHub Actions actions in workflows.
+  # See: https://docs.github.com/code-security/dependabot/working-with-dependabot/keeping-your-actions-up-to-date-with-dependabot
+  - package-ecosystem: "github-actions"
+    directory: "/" # Check the repository's workflows under /.github/workflows/
+    schedule:
+      interval: "weekly"

.github/workflows/codeql.yml

@@ -0,0 +1,71 @@
+# For most projects, this workflow file will not need changing; you simply need
+# to commit it to your repository.
+#
+# You may wish to alter this file to override the set of languages analyzed,
+# or to provide custom queries or build logic.
+#
+# ******** NOTE ********
+# We have attempted to detect the languages in your repository. Please check
+# the `language` matrix defined below to confirm you have the correct set of
+# supported CodeQL languages.
+#
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main" ]
+  schedule:
+    - cron: '56 17 * * 4'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'python' ]
+        # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
+        # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+        # If you wish to specify custom queries, you can do so here or in a config file.
+        # By default, queries listed here will override any specified in a config file.
+        # Prefix the list here with "+" to use these queries and those in the config file.
+
+        # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
+        # queries: security-extended,security-and-quality
+
+
+    # Autobuild attempts to build any compiled languages  (C/C++, C#, Go, or Java).
+    # If this step fails, then you should remove it and run the build manually (see below)
+    - name: Autobuild
+      uses: github/codeql-action/autobuild@v2
+
+    # ℹ️ Command-line programs to run using the OS shell.
+    # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
+
+    #   If the Autobuild fails above, remove it and uncomment the following three lines.
+    #   modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
+
+    # - run: |
+    #   echo "Run, Build Application using script"
+    #   ./location_of_script_within_repo/buildscript.sh
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/commitlint.yml

@@ -9,11 +9,11 @@ jobs:
     name: Check PR title
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-node@v3
         with:
-          node-version: '14'
+          node-version: '16'
       - run: npm install -g --force commitlint @commitlint/cli commitlint-plugin-cleanfeet
       - run: npm install conventional-changelog-conventionalcommits
       - run: touch .git/COMMIT_EDITMSG
-      - run: echo ${{ github.event.pull_request.title }} | commitlint
+      - run: echo "${{ github.event.pull_request.title }}" | commitlint

.github/workflows/publish-sdist.yml

@@ -10,15 +10,15 @@ jobs:
     name: Build and publish on PyPI
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
+      - uses: actions/checkout@v3
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Build a wheel and a source tarball
         run: |
-          pip install setuptools>=42 wheel setuptools_scm[toml]>=3.4
-          python setup.py sdist bdist_wheel
+          pip install setuptools>=42 build setuptools_scm[toml]>=3.4
+          python -m build -o dist
       - name: Publish distribution package to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
         with:

.github/workflows/run-tox.yml

@@ -5,6 +5,7 @@ on:
   push:
     branches:
       - main
+  workflow_dispatch:
 
 jobs:
   build:
@@ -15,28 +16,48 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+    - name: Cache tox and precommit environments
+      uses: actions/cache@v3
+      with:
+        path: |
+          .tox
+          ~/.cache/pre-commit
+        key: ${{ runner.os }}-${{ matrix.python-version }}-${{ steps.date.outputs.date }}-${{ hashFiles('setup.py') }}-${{ hashFiles('.pre-commit-config.yaml') }}
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
         pip install tox-gh-actions
+    - name: Clear results in tox environments
+      run: |
+        rm -rf .tox/*/tmp
     - name: Run tox
       run: |
         tox
     - name: JUnit Report Action
-      uses: mikepenz/action-junit-report@v3.2.0
+      uses: mikepenz/action-junit-report@v3
       if: always() # always run even if the previous step fails
       with:
         report_paths: 'reports/pytest-*.xml'
     - name: Upload to codecov
       if: ${{matrix.python-version == '3.9'}}
-      uses: codecov/codecov-action@v1
+      uses: codecov/codecov-action@v3
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
         flags: pytest
-        name: "NeuroTS"
+        name: "NeuroTS-py${{ matrix.python-version }}"
+    - name: Upload test artifacts
+      uses: actions/upload-artifact@v3
+      if: always()
+      with:
+        name: tests-${{ matrix.python-version }}
+        retention-days: 4
+        path: |
+          .tox/py*/tmp
+          docs/build
+          reports

commitlint.config.js

@@ -25,6 +25,7 @@ module.exports = {
 				'Fix',
 				'Perf',
 				'Refactor',
+				'Release',
 				'Revert',
 				'Style',
 				'Test',
@@ -95,6 +96,11 @@ module.exports = {
 						title: 'Reverts',
 						emoji: '🗑',
 					},
+					Release: {
+						description: 'Release commit',
+						title: 'Release',
+						emoji: '🎉',
+					},
 				},
 			},
 			scope: {

neurots/astrocyte/context.py

@@ -53,6 +53,7 @@ def __init__(self, coordinates):
         self.active = np.ones(len(coordinates), dtype=bool)
 
     def __len__(self):
+        """Return the number of active points."""
         return len(self.active)
 
     @property

neurots/generate/algorithms/common.py

@@ -85,6 +85,7 @@ def __init__(self, bif_id, bif, term_id, term, ref):
         # self.verify()
 
     def __str__(self):
+        """Return the string representation of the TMDStop."""
         return (
             f"(Ref: {self.ref}, BifID: {self.bif_id}, Bif: {self.bif}, TermID: {self.term_id}, "
             f"Term: {self.term})"
@@ -167,6 +168,7 @@ def expected_maximum_length(self):
         return abs(self.ref - max(self.bif, self.term))
 
     def __eq__(self, other):
+        """Check for equality with another object."""
         if isinstance(other, TMDStop):
             return (
                 self.bif_id == other.bif_id

pyproject.toml

@@ -14,7 +14,6 @@ target-version = [
     "py38",
     "py39",
 ]
-include = 'neurots\/.*\.py$|tests\/.*\.py$|doc\/source\/conf\.py$|setup\.py$|examples\/*.py$'
 
 # PYDOCSTYLE
 [tool.pydocstyle]
@@ -24,7 +23,7 @@ add-ignore = [
     "D107",
 ]
 convention = "google"
-match = "[neurots, tests, docs/source/conf.py, setup.py, examples]"
+match = 'neurots\/.*\.py$|docs\/source\/conf\.py$|setup\.py$|examples\/.*.py$'
 
 # ISORT
 [tool.isort]

setup.py

@@ -74,6 +74,7 @@
         "docs": doc_reqs,
         "test": test_reqs,
     },
+    include_package_data=True,
     classifiers=[
         "Development Status :: 4 - Beta",
         "Intended Audience :: Science/Research",
@@ -86,5 +87,4 @@
         "Programming Language :: Python :: 3.11",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
-    include_package_data=True,
 )

tox.ini

@@ -53,10 +53,10 @@ commands =
 [testenv:check-packaging]
 skip_install = true
 deps =
-    wheel
+    build
     twine
 commands =
-    python setup.py sdist bdist_wheel -d {envtmpdir}/dist
+    python -m build -o {envtmpdir}/dist
     twine check {envtmpdir}/dist/*
 
 [testenv:lint]
@@ -75,13 +75,14 @@ deps =
     codespell
     pre-commit
 commands =
-    codespell -i 2 -x .codespellignorelines -w {[base]files} README.md CHANGELOG.md
+    codespell -i 3 -x .codespellignorelines -w {[base]files} README.md CHANGELOG.md docs/source
     pre-commit run --all-files
 
 [testenv:docs]
 changedir = docs
 extras = docs
-allowlist_externals = make
+allowlist_externals =
+    make
 # set warnings as errors using the -W sphinx option
 commands =
     make clean